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* Issue #1071: add yapf configuration file * yapf formatting of Code directory * yapf formatting of Contrib directory * yapf formatting of Data directory * yapf formatting of Docs directory * yapf formatting of External directory * yapf formatting of Projects directory * yapf formatting of Regress directory * yapf formatting of Scripts directory * yapf formatting of Web directory * yapf formatting of rdkit directory
102 lines
3.9 KiB
Python
102 lines
3.9 KiB
Python
#
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# Copyright (c) 2009, Novartis Institutes for BioMedical Research Inc.
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are
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# met:
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#
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above
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# copyright notice, this list of conditions and the following
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# disclaimer in the documentation and/or other materials provided
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# with the distribution.
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# * Neither the name of Novartis Institutes for BioMedical Research Inc.
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# nor the names of its contributors may be used to endorse or promote
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# products derived from this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Created by Greg Landrum and Anna Vulpetti, March 2009
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from rdkit import Chem
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from rdkit import DataStructs
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from CreateFps import GetMolFingerprint
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from rdkit.RDLogger import logger
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logger = logger()
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import sys
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# maxPathLength is the maximum path length in atoms
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# maxPathLength=6 corresponds to F-FP-5
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# maxPathLength=7 corresponds to F-FP-6
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# maxPathLength=8 corresponds to F-FP-7
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maxPathLength = 8
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# nameField is the name of the property (from the SD file) that has molecule
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# names... If the molecules have names in the first row of the file, use "_Name"
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nameField = 'Compound_orig'
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#nameField = '_Name'
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# propField is the name of the property (from the SD file) you want to use
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# as the "activity"
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propField = 'chemical_shift_1'
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# similarity threshold for a pair to be considered interesting.
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# (i.e. pairs with a similiarity below this value will not be
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# added to the output.
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similarityThreshold = 0.5
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if __name__ == '__main__':
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suppl = Chem.SDMolSupplier(sys.argv[1])
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outF = file(sys.argv[2], 'w+')
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data = []
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logger.info('reading molecules and generating fingeprints')
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for i, mol in enumerate(suppl):
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if not mol:
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continue
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smi = Chem.MolToSmiles(mol, True)
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nm = mol.GetProp(nameField)
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property = float(mol.GetProp(propField))
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fp = GetMolFingerprint(mol, maxPathLength)
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data.append((nm, smi, property, fp))
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logger.info(' got %d molecules' % len(data))
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logger.info('calculating pairs')
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pairs = []
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for i in range(len(data)):
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for j in range(i + 1, len(data)):
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if DataStructs.DiceSimilarity(data[i][-1], data[j][-1]) > similarityThreshold:
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pairs.append((i, j))
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if not (i + 1) % 100:
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logger.info('Done %d molecules' % (i + 1))
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logger.info(' got %d reasonable pairs' % len(pairs))
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logger.info('creating output file')
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print >> outF, 'nameA|nameB|nameAB|smilesA|smilesB|smilesAB|actA|actB|dAct|dist|disparity'
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for i, j in pairs:
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if data[i][2] < data[j][2]:
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i, j = j, i
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nmi, smii, propi, fpi = data[i]
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nmj, smij, propj, fpj = data[j]
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dAct = propi - propj
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dist = 1. - DataStructs.DiceSimilarity(fpi, fpj)
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if dist != 0:
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disparity = dAct / dist
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else:
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disparity = 1000
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print >> outF, '%s|%s|%s_%s|%s|%s|%s.%s|%f|%f|%f|%f|%f' % (
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nmi, nmj, nmi, nmj, smii, smij, smii, smij, propi, propj, dAct, dist, disparity)
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